Abstract

This report summarizes the output of population genetic analyses of a pool-seq RAD library.

Filtering

Stepwise filtering reuslts

SNPs remaining after each filtering step.
Note: filtering results displayed are independent, not cumulative.
Filter options with no effect: max_missing, min_mean_depth, min_pools.

Cumulative filtering results

SNPs remaining after each filtering step.
Cumulative filter results
(Note: filtered SNP count may differ from SNP counts associated with Fst calculations).

High-level summaries

grenedalf

All SNPs

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

SNPs shared by all pools

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

poolfstat

All SNPs

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

SNPs shared by all pools

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

popoolation

All SNPs

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

SNPs shared by all pools

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

Pairwise Fst by minimum coverage

grenedalf

All SNPs

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

SNPs shared by all pools

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

poolfstat

All SNPs

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

SNPs shared by all pools

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

popoolation

All SNPs

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

SNPs shared by all pools

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

Summary statistic heatmaps

grenedalf

All SNPs

Fst (±SD)

Lower triangle: mean pairwise Fst
Upper triangle: standard deviation of Fst
Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to Fst calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation
Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs
Note: Grey cells indicate missing data.

SNPs shared by all pools

Fst (±SD)

Lower triangle: mean pairwise Fst
Upper triangle: standard deviation of Fst
Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to Fst calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation
Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs
Note: Grey cells indicate missing data.

poolfstat

All SNPs

Fst (±SD)

Lower triangle: mean pairwise Fst
Upper triangle: standard deviation of Fst
Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to Fst calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation
Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs
Note: Grey cells indicate missing data.

SNPs shared by all pools

Fst (±SD)

Lower triangle: mean pairwise Fst
Upper triangle: standard deviation of Fst
Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to Fst calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation
Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs
Note: Grey cells indicate missing data.

popoolation

All SNPs

Fst (±SD)

Lower triangle: mean pairwise Fst
Upper triangle: standard deviation of Fst
Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to Fst calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation
Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs
Note: Grey cells indicate missing data.

SNPs shared by all pools

Fst (±SD)

Lower triangle: mean pairwise Fst
Upper triangle: standard deviation of Fst
Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to Fst calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation
Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs
Note: Grey cells indicate missing data.

Fst method correlations

grenedalf vs poolfstat

Note: Due to potentially large datasets, only a subsample of 1,000 Fst values is shown here.

grenedalf vs popoolation

Note: Due to potentially large datasets, only a subsample of 1,000 Fst values is shown here.

poolfstat vs popoolation

Note: Due to potentially large datasets, only a subsample of 1,000 Fst values is shown here.

Fisher’s test plots

Fisher test results are presented as static plots since these datasets can get huge, making plotly go slow or crash.

assesspool

Points above red line indicate p < 0.05.

Fisher's exast test p-values for coverage ≥10

popoolation

Points above red line indicate p < 0.05.

Fisher's exast test p-values for coverage ≥10